eicm (version 1.0.3)

confint.eicm: Confidence intervals for EICM parameters

Description

Computes the profile (penalized) likelihood confidence intervals for all estimated parameters in a EICM model. If the likelihood profiles are not computed yet, they will be computed first.

Usage

# S3 method for eicm
confint(
  object,
  parm,
  level = 0.99,
  step = 0.3,
  ncores = parallel::detectCores(),
  ...
)

Value

The same model object with a new confint component.

Arguments

object

the fitted EICM model.

parm

currently unused.

level

the confidence level required.

step

the step increments/decrements at which to compute the likelihood profile points.

ncores

the number of CPU cores to use when computing profiles for all parameters.

...

additional argument(s) for methods

Examples

# \donttest{
# load the included parameterized model
data(truemodel)

# realize the model
occurrences <- predict(truemodel, nrepetitions=1)

# fit the model without species interactions
fitted <- eicm(occurrences, n.latent=2, mask.sp=0, do.selection=FALSE)$fitted.model

# compute confidence intervals for all parameters
# this updates the fitted model with the confints
fitted <- confint(fitted, ncores=2)

# plot the confidence intervals
plot(fitted, type="confint")
# }